The Dimanganese(II) Site of Bacillus subtilis Class Ib Ribonucleotide Reductase
Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, Mn[III over 2]-Y[superscript •], in their homodimeric NrdF (β2) subunit to initiate reduction of ribonucleotides to deoxyribonucleotides. The structure of the Mn[II over 2] form of NrdF is an important component in...
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American Chemical Society (ACS)
2013
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| Online Access: | http://hdl.handle.net/1721.1/82564 https://orcid.org/0000-0001-8076-4489 |
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| author | Boal, Amie K. Cotruvo, Joseph A. Stubbe, JoAnne Rosenzweig, Amy C. |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Boal, Amie K. Cotruvo, Joseph A. Stubbe, JoAnne Rosenzweig, Amy C. |
| author_sort | Boal, Amie K. |
| collection | MIT |
| description | Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, Mn[III over 2]-Y[superscript •], in their homodimeric NrdF (β2) subunit to initiate reduction of ribonucleotides to deoxyribonucleotides. The structure of the Mn[II over 2] form of NrdF is an important component in understanding O[subscript 2]-mediated formation of the active metallocofactor, a subject of much interest because a unique flavodoxin, NrdI, is required for cofactor assembly. Biochemical studies and sequence alignments suggest that NrdF and NrdI proteins diverge into three phylogenetically distinct groups. The only crystal structure to date of a NrdF with a fully ordered and occupied dimanganese site is that of Escherichia coli Mn[II over 2]-NrdF, prototypical of the enzymes from actinobacteria and proteobacteria. Here we report the 1.9 Å resolution crystal structure of Bacillus subtilis Mn[II over 2]-NrdF, representative of the enzymes from a second group, from Bacillus and Staphylococcus. The structures of the metal clusters in the β2 dimer are distinct from those observed in E. coli Mn[II over 2]-NrdF. These differences illustrate the key role that solvent molecules and protein residues in the second coordination sphere of the Mn[II over 2] cluster play in determining conformations of carboxylate residues at the metal sites and demonstrate that diverse coordination geometries are capable of serving as starting points for Mn[III over 2]-Y[superscript •] cofactor assembly in class Ib RNRs. |
| first_indexed | 2024-09-23T16:55:03Z |
| format | Article |
| id | mit-1721.1/82564 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T16:55:03Z |
| publishDate | 2013 |
| publisher | American Chemical Society (ACS) |
| record_format | dspace |
| spelling | mit-1721.1/825642022-09-29T22:23:46Z The Dimanganese(II) Site of Bacillus subtilis Class Ib Ribonucleotide Reductase Boal, Amie K. Cotruvo, Joseph A. Stubbe, JoAnne Rosenzweig, Amy C. Massachusetts Institute of Technology. Department of Biology Massachusetts Institute of Technology. Department of Chemistry Cotruvo, Joseph A. Stubbe, JoAnne Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, Mn[III over 2]-Y[superscript •], in their homodimeric NrdF (β2) subunit to initiate reduction of ribonucleotides to deoxyribonucleotides. The structure of the Mn[II over 2] form of NrdF is an important component in understanding O[subscript 2]-mediated formation of the active metallocofactor, a subject of much interest because a unique flavodoxin, NrdI, is required for cofactor assembly. Biochemical studies and sequence alignments suggest that NrdF and NrdI proteins diverge into three phylogenetically distinct groups. The only crystal structure to date of a NrdF with a fully ordered and occupied dimanganese site is that of Escherichia coli Mn[II over 2]-NrdF, prototypical of the enzymes from actinobacteria and proteobacteria. Here we report the 1.9 Å resolution crystal structure of Bacillus subtilis Mn[II over 2]-NrdF, representative of the enzymes from a second group, from Bacillus and Staphylococcus. The structures of the metal clusters in the β2 dimer are distinct from those observed in E. coli Mn[II over 2]-NrdF. These differences illustrate the key role that solvent molecules and protein residues in the second coordination sphere of the Mn[II over 2] cluster play in determining conformations of carboxylate residues at the metal sites and demonstrate that diverse coordination geometries are capable of serving as starting points for Mn[III over 2]-Y[superscript •] cofactor assembly in class Ib RNRs. United States. Dept. of Energy (Contract DE-AC02-06CH11357) Michigan Economic Development Corporation (Michigan Technology Tri-Corridor Grant 085P1000817) National Cancer Institute (U.S.) (Y1-CO-1020) National Institute of General Medical Sciences (U.S.) (Y1-GM-1104) 2013-11-25T13:04:43Z 2013-11-25T13:04:43Z 2012-03 2012-03 Article http://purl.org/eprint/type/JournalArticle 0006-2960 1520-4995 http://hdl.handle.net/1721.1/82564 Boal, Amie K., Joseph A. Cotruvo, JoAnne Stubbe, and Amy C. Rosenzweig. “The Dimanganese(II) Site of Bacillus subtilis Class Ib Ribonucleotide Reductase.” Biochemistry 51, no. 18 (May 8, 2012): 3861-3871. https://orcid.org/0000-0001-8076-4489 en_US http://dx.doi.org/10.1021/bi201925t Biochemistry Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf American Chemical Society (ACS) PMC |
| spellingShingle | Boal, Amie K. Cotruvo, Joseph A. Stubbe, JoAnne Rosenzweig, Amy C. The Dimanganese(II) Site of Bacillus subtilis Class Ib Ribonucleotide Reductase |
| title | The Dimanganese(II) Site of Bacillus subtilis Class Ib Ribonucleotide Reductase |
| title_full | The Dimanganese(II) Site of Bacillus subtilis Class Ib Ribonucleotide Reductase |
| title_fullStr | The Dimanganese(II) Site of Bacillus subtilis Class Ib Ribonucleotide Reductase |
| title_full_unstemmed | The Dimanganese(II) Site of Bacillus subtilis Class Ib Ribonucleotide Reductase |
| title_short | The Dimanganese(II) Site of Bacillus subtilis Class Ib Ribonucleotide Reductase |
| title_sort | dimanganese ii site of bacillus subtilis class ib ribonucleotide reductase |
| url | http://hdl.handle.net/1721.1/82564 https://orcid.org/0000-0001-8076-4489 |
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